Contacts of the strand formed by residues 1029 - 1035 (chain K) in PDB entry 3F5P
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG1029 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1003K ARG* 5.3 2.4 - - - +
1015K GLU* 2.7 33.5 + - - +
1016K GLY 3.6 8.3 - - - +
1017K VAL* 4.8 10.5 - - + +
1028K THR* 1.3 81.2 - - - +
1030K VAL* 1.3 63.1 + - - +
1080K GLU* 4.8 0.5 - - - -
1081K LEU* 3.3 37.9 + - + +
1083K THR* 3.6 22.4 - - - +
1145K GLU* 4.4 11.7 + - - +
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Residues in contact with VAL1030 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1015K GLU* 3.6 2.1 - - - +
1016K GLY 2.8 42.7 + - - +
1018K ALA* 3.6 22.0 - - + -
1028K THR* 3.4 13.5 - - + +
1029K ARG* 1.3 81.2 - - - +
1031K ALA* 1.3 59.2 + - - +
1032K ILE* 3.5 30.7 - - + -
1066K LEU* 3.7 17.0 - - + -
1078K ILE* 3.7 17.3 - - + -
1079K MET 3.3 9.6 - - - +
1081K LEU* 3.6 16.3 - - - +
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Residues in contact with ALA1031 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K 741 3.7 55.7 - - + +
1005K LEU* 4.5 2.2 - - + -
1013K VAL* 4.2 4.3 - - + -
1014K TYR 3.4 7.6 - - - +
1030K VAL* 1.3 71.8 - - - +
1032K ILE* 1.3 66.8 - - - +
1078K ILE* 3.5 0.9 - - - -
1079K MET* 2.8 34.6 + - + +
1081K LEU* 4.0 5.6 - - + +
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Residues in contact with ILE1032 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K 741 4.1 0.9 - - - -
999K ILE* 3.2 28.7 - - + -
1000K THR 4.6 1.3 - - - +
1001K MET* 4.0 17.5 - - + -
1012K MET 3.9 0.9 - - - +
1013K VAL* 3.5 2.5 - - - +
1014K TYR* 2.7 47.1 + - + +
1015K GLU 5.0 0.2 - - - -
1016K GLY* 4.4 13.2 - - - +
1017K VAL 4.9 0.2 - - - +
1030K VAL* 3.5 25.6 - - + +
1031K ALA* 1.3 80.4 - - - +
1033K LYS* 1.3 63.0 + - - +
1076K LEU* 4.0 34.5 - - + -
1077K VAL 3.5 8.7 - - - +
1078K ILE* 4.3 8.3 - - + -
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Residues in contact with LYS1033 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K 741 3.4 57.2 + - + +
1008K GLY* 3.5 5.0 - - - -
1009K SER* 2.6 40.6 + - - +
1010K PHE* 3.2 25.4 - - - +
1011K GLY* 3.5 14.8 - - - +
1012K MET 3.2 12.1 - - - +
1013K VAL* 4.3 5.4 - - + +
1032K ILE* 1.3 73.8 - - - +
1034K THR* 1.3 69.0 + - - +
1035K VAL* 4.7 0.8 - - + +
1047K PHE* 3.9 11.0 - - + -
1075K THR 3.5 1.4 - - - +
1076K LEU* 3.4 8.7 - - - +
1077K VAL* 3.1 30.7 + - + +
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Residues in contact with THR1034 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1001K MET* 3.5 33.9 - - + -
1011K GLY* 3.3 23.4 - - - -
1012K MET* 3.1 11.3 + - - +
1014K TYR* 4.1 18.2 - - + -
1033K LYS* 1.3 74.3 - - - +
1035K VAL* 1.3 62.0 + - - +
1036K ASN* 4.0 3.9 + - - +
1074K PRO* 4.4 14.1 - - + -
1075K THR 3.6 3.8 - - - -
1076K LEU* 3.6 17.5 - - + -
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Residues in contact with VAL1035 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010K PHE* 4.2 25.4 - - + +
1011K GLY* 5.0 0.2 - - - -
1033K LYS* 4.7 2.9 - - + -
1034K THR* 1.3 75.8 - - - +
1036K ASN* 1.3 63.8 + - - +
1039K ALA* 3.8 25.6 - - + -
1043K GLU* 5.8 1.1 - - - +
1044K ARG* 3.6 22.0 + - + +
1047K PHE* 3.2 47.8 - - + -
1074K PRO* 3.5 3.1 - - - +
1075K THR* 3.1 35.1 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il